[BioSQL-l] GBrowse on BioSQL dead in water again

[Lincoln Stein]

I've updated the GBrowse and DAS release notes to tell people to check out he 
bioperl-release-1-1-0 branch of biosql.  Probably safest thing to do.

Lincoln

On Wednesday 09 October 2002 03:51 am, Elia Stupka wrote:
> Hi Hilmar and Lincoln,
>
> Hilmar note that the problem is precisely the fact that Lincoln relied on a
> branch module, which BioDatabaseAdaptor. This module was the most
> straightforward way to call one new method (not a cascade of objects and
> methods) to do both a)connection to a biosql database and b)getting the
> adaptor for one particular biological database.
>
> Das was already working off biosql thanks to the work that Lincoln did and
> GBrowse was already running nicely on the DasI interface to a single
> biological database within biosql.
>
> So all is needed is *not to remove* that object, and all would be back to
> normal.
>
> Elia
>
>
> ----- Original Message -----
> From: "Hilmar Lapp" <hlapp@gnf.org>
> To: <lstein@cshl.org>; "elia@gugu-sg.org" <elia@fugu-sg.org>
> Cc: <bioperl-l@bio.perl.org>; <biosql-l@open-bio.org>
> Sent: Wednesday, October 09, 2002 5:29 AM
> Subject: RE: [BioSQL-l] GBrowse on BioSQL dead in water again
>
> > For production work do not use the head of bioperl-db nor biosql-schema.
>
> Use the branch bioperl-release-1-1-0 from both modules (I did announce this
> on both lists). That branch has the API unchanged and the schema only
> changed where it shouldn't break existing adaptors (if there are changes
> which do break adaptors, I'll fix this on the branch, unless the adaptor
> broke because it was using '*' as the select list).
>
> > I have yet to re-introduce DAS support into the main trunk. I'd
> > appreciate
>
> any help or advice for doing this (what do I need to look at or implement),
> as it will be helpful for us here as well.
>
> > Also, if anyone wants to volunteer taking this on, I'll be more than glad
>
> to explain how the adaptors now work. I hesitated doing this on the list
> yet because I've just started running tests on a larger scale (dumping
> swissprot now works), and changes may or may not become necessary.
>
> > As a brief status report, all tests in t/ pass except for one (test, not
>
> script) which tests for DBLink::optional_id, which is unsupported right
> now. As for the adaptors and schema support, the (subjectively) important
> parts work. What doesn't work so far comprises of remote locations, fuzzy
> locations, sub-seqfeatures, ontology relationships, and qualifiers for
> dbxrefs. That these don't work means the respective information will be
> lost and not stored; it will not crash a script or report an error.
>
> > Also, there is only mysql support for now. I'm going to start porting
>
> driver specific code to oracle today or tomorrow. I'll take on Postgres
> only after that. Again, anyone willing to volunteer is greatly welcome and
> I'll explain what needs to be done.
>
> > On a separate note, be aware that the biosql schema on the main trunk is
>
> not fully stable yet. I have a couple more change requests pending that
> I'll post soon. I'll adapt the bioperl-db adaptors for all of such schema
> changes.
>
> > -hilmar
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> > > -----Original Message-----
> > > From: Lincoln Stein [mailto:lstein@cshl.org]
> > > Sent: Tuesday, October 08, 2002 1:16 PM
> > > To: elia@gugu-sg.org
> > > Cc: bioperl-l@bio.perl.org; biosql-l@open-bio.org
> > > Subject: [BioSQL-l] GBrowse on BioSQL dead in water again
> > >
> > >
> > > Hi Elia,
> > >
> > > Alas, the latest CVS update of bioperl-db removed the
> > > Bio::DB::BioSQL::BioDatabaseAdaptor module, and so broke the
> > > Bio::DB::Das::BioSQL module that was dependent upon it.  There is no
> > > obvious documentation of what the preferred interface now is.  Could
> > > you show me how to rewrite the following script for me to use the
> > > approved API?
> > >
> > > I had been running GBrowse very happily on top of it until now, but
> > > I'm afraid that it is now dead in the water.
> > >
> > > Thanks,
> > >
> > > Lincoln
> > >
> > > -----------
> > >
> > > #!/usr/bin/perl
> > >
> > > use Bio::DB::BioSQL::BioDatabaseAdaptor;
> > > use Bio::DB::BioSeqDatabase;
> > >
> > > my $dbc = Bio::DB::BioSQL::BioDatabaseAdaptor->new_from_registry(
> > >     driver   => 'mysql',
> > >     dbname => 'biosql',
> > >     biodbname => 'test',
> > >     host   =>
> > > 'localhost',
> > >     user   => 'lstein',
> > >     pass   => undef,
> > >     port   => undef,
> > >      );
> > > my @seq = $dbc->get_all_primary_ids;
> > > print "got @seq\n";
> > >
> > > my $thing = $dbc->get_Seq_by_acc($seq[0]);
> > > print "got $thing\n";
> > >
> > > my @a = $thing->top_SeqFeatures;
> > >
> > > my $ad = $dbc->_adaptor;
> > > print $ad->list_bioentry_ids('test'),"\n";
> > >
> > > --
> > > ==============================================================
> > > ==========
> > > Lincoln D. Stein                           Cold Spring Harbor
> > > Laboratory
> > > lstein@cshl.org                   Cold
> > > Spring Harbor, NY
> > > Positions available at my lab: see http://stein.cshl.org/#hire
> > > ==============================================================
> > > ==========
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